feat/data api (#70)

* feat: added support for materialized views
           added rfamily_counts

model/data.py

@@ -14,15 +14,21 @@
 }
 
 # no auto-primary_keys due to permissions (?)
-def model_from_table(name, __tablename__=None, primary_keys=None):
+def model_from_table(name, __tablename__=None, columns=None, primary_keys=None):
     if(__tablename__ is None):
         __tablename__ = name
 
-    connection = SQLAlchemyEngine.connect()
-
-    stmt = 'SELECT column_name, data_type FROM information_schema.columns WHERE table_schema = \'public\' AND table_name = \'' + __tablename__ + '\' ORDER BY ordinal_position ASC;'
-    columns = connection.execute(stmt).all()
-    connection.close()
+    if(columns is None):
+        connection = SQLAlchemyEngine.connect()
+        stmt = 'SELECT column_name, data_type FROM information_schema.columns WHERE table_schema = \'public\' AND table_name = \'' + __tablename__ + '\' ORDER BY ordinal_position ASC;'
+        columns = connection.execute(stmt).all()
+
+        if(len(columns) == 0):
+            # try a materialized view
+            stmt = 'SELECT attname AS column_name, format_type(atttypid, atttypmod) AS data_type FROM pg_attribute WHERE attrelid = \'' + __tablename__ + '\'::regclass AND attnum > 0;'
+            columns = connection.execute(stmt).all()
+
+        connection.close()
 
     for key, value in columns:
         if value not in type_to_sqlalchemy_type:

route/data.py

@@ -70,6 +70,8 @@ def verify_password(username, password):
     'dsequence': model_from_table(name='dsequence', primary_keys=('run_id')),
     'dsra': model_from_table(name='dsra', primary_keys=('run_id')),
     'rfamily': model_from_table(name='rfamily', primary_keys=('run_id')),
+    # 'rfamily_counts': model_from_table(name='rfamily_counts', columns=[('family_name', 'text'), ('score', 'bigint'), ('percent_identity', 'bigint'), ('count', 'bigint')], primary_keys=('family_name')),
+    'rfamily_counts': model_from_table(name='rfamily_counts', primary_keys=('family_name')),
     'rphylum': model_from_table(name='rphylum', primary_keys=('run_id')),
     'rsequence': model_from_table(name='rsequence', primary_keys=('run_id')),
     'rsra': model_from_table(name='rsra', primary_keys=('run_id')),
@@ -127,6 +129,15 @@ def data_query(arguments):
     data_session.close()
 
     if('_count' in arguments):
+        print('memoize query')
+        stmt = 'SELECT count(*) as count_1 FROM(' + sub('\n', '', str(data_query.statement.compile(dialect=postgresql.dialect()))) + ') AS anon_1'
+        stmt_md5 = md5(stmt.encode('utf-8')).hexdigest()
+        print('-->', stmt, stmt_md5)
+
+        # check if it's there
+        # if it's not calculate and store
+        # return value
+
         return (
             data_query
                 .count()